Agreed. But I really didn't get a chance to look in the boot. But I think the regular MX-5 has a “dedicated” storage space behind the seats for the cloth top to fold into, that doesn’t really affect the boot. If that’s the case with the hard top folder, it seems like a lot of wasted space with the top up.
My sister is looking at getting the new G6 (GT preferably) with the folding hard top. Looking at that car's boot I was surprised at how much space still remains even with the top down. Problem is you probably don’t want to load up the trunk, then fold the top away, because the back wall expands with the top down and you might break something.
Other than the added security I really don't see any advantage to the hard top.